A novel strategy for the preparation of the organic-inorganic hybrid boronate affinity monolith was developed via the "thiol-ene" click reaction. A thiol group-modified silica monolith was first synthesized via the sol-gel process by the in situ co-condensation with tetramethoxysilane (TMOS) and 3-mercaptopropyltrimethoxysilane (MPTMS) as precursors. Then 3-acrylamidophenylboronic acid (AAPBA) was covalently immobilized on the hybrid monolith via the "thiol-ene" click reaction to form AAPBA-silica hybrid affinity monolith. The reaction conditions for the preparation of AAPBA-silica hybrid affinity monolith were optimized, including the ratio of TMOS to MPTMS, the contents of poly(ethylene glycol) (PEG) and methanol. The morphology and mechanical stability of the boronate affinity monolith were characterized and evaluated by scanning electron microscopy and Fourier-transform infrared spectroscopy. The obtained boronate affinity hybrid monolith exhibited excellent specificity toward the nucleosides containing cis-diols under neutral conditions. It was further applied to the specific capture of the glycoproteins ovalbumin and horseradish peroxidase. The method is novel and reliable, which has a great potential for the preparation of different kinds of the boronate affinity monoliths.